PB2390: STUDY OF GENETIC ALTERATIONS USING A CUSTOM LYMPHOID TARGETED NGS PANEL IN PATIENTS WITH FOLLICULAR LYMPHOMA: A PILOT STUDY
Authors: Евгений Куневич, Irina Martynkevich, Ekaterina Motyko, Maria Mikhaleva, Sergey Voloshin, Sergey Sidorkevich
Journal: HemaSphere (2023)

Topic: 20. Lymphoma Biology & Translational Research Background: Follicular lymphoma (FL) is a morphologically and clinically heterogeneous disease, which, in addition to t(14;18), is characterized by changes in genes involved in various intracellular processes. At present, the identification of new molecular markers has become possible with the introduction of the NGS method into clinical practice. Aims: To study the patterns of genetic changes in patients with follicular lymphoma using a custom lymphoid targeted NGS panel. Methods: An NGS study was performed on 25 patients (median age 54 years) with morphologically confirmed follicular lymphoma using the original targeted lymphoid panel, including 118 genes, on the NextSeq platform (Illumina, USA) using the paired end reading method. The clinical significance of mutations was determined using the COSMIC, ClinVar, gnomAD databases using in silico analysis. Results: All examined patients had genetic aberrations. A total of 128 mutations of clinical significance were identified in 48 genes. The average number of mutations in 1 gene was 2.7 (95% CI: 1.9-3.4). The highest mutation frequency was noted in the genes: KMT2C – 52%, KMT2D – 48%, CREBBP – 32%, NOTCH2 – 32%, GNAS – 24%, FAT1, ITPKB and KDR – 20% each. Missense mutations occurred with a frequency of 83.6%, nonsense – 5.5%, synonymous – 4.7%, frameshift mutations – 4.9%, others – 2.3%. The median variant allele frequency (VAF) was 8.96% (25th and 75th percentiles: 3.83-36.77%). In order to determine the relationship between genetic events, a matrix of pairwise correlations was built (Fig. 1A). Hierarchical cluster analysis was applied to the resulting matrix to identify clusters of co-associated genetic changes. All mutated genes were then subjected to gene set enrichment analysis (GSEA) using Metascape (data source: GO, KEGG, Reactome, WikiPathways). In total, GSEA analysis revealed 675 possible annotated biological processes involving 3 or more genes at p < 0.05. The most enriched pathways in the analysis associated with oncogenesis were: regulation of cell activation (clusters 1, 3, 5, -log(q-value) = 11.2), chromatin organization (clusters 2, 4, 5, -log(q -value) = 9.1), histone modification (clusters 2, 4, 5, -log(q-value) = 7.7), JAK-STAT signaling pathway (clusters 4, 5, -log(q-value) = 6.8), MAPK cascade (clusters 1, 4, 5, -log(q-value) = 6.4), cell proliferation (clusters 3, 4, 5, -log(q-value) = 6.4), NF-kB signaling pathway (cluster 5, -log(q-value) = 5.4), etc. (Fig. 1B). Notably, mutations in the MYC, EP300, MYD88, CREBBP, ATM, and BCL2 genes can lead to deregulation in several signaling pathways, mediating more complex molecular changes in FL cells (Fig. 1C). Most mutations in transcriptional regulation genes result in an increase in protein function. Two-year progression-free and event-free survival in patients with at least one mutation in these genes was shown to be better than in patients without mutations (66% [95% CI: 38–88] vs. 40% [95% CI: 12–74], p = 0.069 and 57% [95% CI: 27–79] vs. 40% [95% CI: 12–74], p = 0.123, respectively). Summary/Conclusion: It was shown that genes involved in chromatin modification KMT2C, KMT2D, CREBBP, etc., are more likely to mutate in FL. Analysis of the functional enrichment of the gene set revealed a significant association of FL with chromatin remodeling pathways, PI3K-AKT and JAK-STAT.Keywords: Mutation analysis, Follicular lymphoma, Gene mutation, Epigenetic